DNA Based Diagnostics and Treatment

1. DNA Based Diagnostics and Treatment Names: Anam Quraishi, Andrew Girgis, Qurat-Ul-Ain Jalal September 23rd, 2013 PHM142 Fall 2014 Instructor: Dr. Jeffrey Henderson

2. Case Study • A recently diagnosed breast cancer patient is in the inpatient oncology department, with a hospital pharmacist who specializes in breast cancer. • She wants to know if she is eligible to participate in a novel clinical trial. • She is in need of relevant information on how the clinical trial will work and how it will benefit her. • How can we help!?!

3. Next Generation Sequencing! • The bases in a small fragment of DNA are sequentially identified from signals emitted as each fragment is re-synthesized from a DNA template strand • Produces millions of sequences in a parallel fashion • Unlike other proceses which are limited to just a few DNA fragments • Produces hundreds of gigabases of data in a single sequencing run • Low cost, high throughput alternative

4. Next Generation Sequencing! • Powerful tool for whole genome sequencing in lab environment • Using prior technology, sequencing an entire genome required a lot of time & resources • NGS allows for a whole genome to be sequenced in a few days • Scalability allows for it to be useful for viral/bacterial genomes along with large human genomes • Allows for better understanding of genetic mutations

5. Detection of Mutations in Cancer • Need reliable detection of mutations within an individual cancer genome • Current techniques include: immunohistochemistry, histological analysis, PCR and traditional sequencing • NGS allows for detailed information on individual tumours • Decrease in cost and increase in accuracy of sequencing with NGS • Future of cancer genomics is underpinned by NGS • The Cancer Genome Atlas: catalogue of genetic mutations responsbile for cancer

6. Detection of Mutations in Cancer • DNA-based diagnostic tests could determine the sites of methylation on tumor suppresor genes which leads to their silencing, and contributes to the development of cancerous tumors. • Development of drugs that prevent this methylation might be used for therapeutic means. • The progression of the disease state can also be monitored by this efficient DNA-based diagnostic test.

7. Detection of Other Diseases • Schizophrenia • Cardiovascular Diseases • Metabolic Disorders • Infectious Diseases (AIDS, tuberculosis, Hepatitis C, Lyme Disease) • Sexually transmitted diseases (Pappiloma virus, chlamydia, herpes) • Presense of bacteria or virus in a specimen • Prenatal diagnosis of genetic disorders • More!

8. Other DNA-based diagnostic methods • PCR (real-time PCR, quantitative PCR, reverse transcriptase PCR, etc.) • Traditional sequencing • Microarrays (Single Nucelotide Polymorphism oligomicroarrays, array comparative hybridization, fluorescence in-situ hybridization) • Southern Blotting

9. How is this relevant for Pharmacists? • Pharma companies are interested in knowing how their drug will affect the disease at the molecular level. • Pharmacists need to be able to counsel patients on personalized medications, based on the diagnosis made by these dna-based diagnostic methods. • DNA-based diagnostics tests are a fast and efficient way to detect, and also monitor the progression of disease or impact of drugs.

10. Closing the case • Identify's patients eligibility for the clinical trail and refer patient to enrol in the clinical trial, if applicable. • NGS identified patient's tumor harbours PIK3CA mutation (prevalent in about 36% of breast cancers) • Also utilizing NGS, a luminal A expression subtype was confirmed (ER+/ERRB2+ and PR+ and HER2 negative) • Favourable prognosis out of breast cancer subtypes (slow growing and non-invasive)

11. Summary Slide • Next Generation Sequencing: The bases in a small fragment of DNA are sequentially identified from signals emitted as each fragment is re-synthesized from a DNA template strand • Advantages: whole genome sequencing in a matter of days, low cost, high accuracy. Sequences millions of DNA fragments concurrently • Diagnostically useful for: Cancers, infectious diseases, metabolic disorders, prenatal diagnosis, identifying presence of virus or bacteria, etc. • Other diagnostic methods : PCR, microarrays, southern blotting • Relevance to Pharmacists: personalized medicine, designing specific drugs and studying their effects, monitoring disease states, counselling .

12. References • D. M. Vasudevan, S. Sreekumari, Kannan Vaidyanathan, Textbook of Biochemistry for Medical Students (text book link can be found here: http://books.google.ca/books?id=nQz8AAAAQBAJ&pg=PA639&lpg=PA639&dq=biochemistry+of+PCR+for+cancer+detection&source=bl&ots=--x4F8nIbx&sig=n6s5PK9lGg7jYwMre37LaVyVYMs&hl=en&sa=X&ei=TegYVNjuKPiIsQStxoGACQ&ved=0CEgQ6AEwBQ#v=onepage&q=biochemistry%20of%20PCR%20for%20cancer%20detection&f=false) • Idris, S. F., Ahmad, S. S., Scott, M. A., Vassiliou, G. S., & Hadfield, J. (2013). The role of high-throughput technologies in clinical cancer genomics. Expert review of molecular diagnostics, 13(2), 167-181. • Simon, R., & Roychowdhury, S. (2013). Implementing personalized cancer genomics in clinical trials. Nature Reviews Drug Discovery, 12(5), 358-369. • http://res.illumina.com/documents/products/illumina_sequencing_introduction.pdf • Magdalena Cizkova et al. (2012) PIK3CA mutation impact on survival in breast cancer patients and in ERα, PR and ERBB2-based subgroups. Breast Cancer Research and Treatment, 14:R28. • http://www.cancer.gov/clinicaltrials/search/view?cdrid=742660&version=HealthProfessional